The closest part of the story that has to do with Columbia University is that Obama claimed to go to the library. Was it the Columbia school library or some other library or somewhere else? Boerner is quoted below:
"Barack has said that he spent a lot of time in the library while at Columbia and one reason for this was that our apartment had irregular heat, and we didn’t enjoy hanging out there once the weather got cold. "
So Boerner really didn't see Barack Obama at the Columbia Library because Obama told him that he went to some library.
The only thing that Boerner attested to while they lived together is just that - being roommates in some private apartment off campus. This story does not prove or even come close that Obama went to school at Columbia University.
Check the URL. The story appears in Columbia College's alumni magazine. It's as close to proof as you are going to get without convening a court, swearing in witnesses, and subpoenaing records.
Consider how Columbia College would look if the story were shown to be what Rev. Manning maintains it is.